Phylogenetic analysis and predicted functional effect of protein mutations of E6 and E7 HPV16 strains isolated in Indonesia
DOI:
https://doi.org/10.13181/mji.v24i4.1197Keywords:
cervical cancer, E6 & E7 gene, E6 & E7 proteins, HPV16 variant, phylogenetic, SNAPAbstract
Background: E6 and E7 are oncoproteins of HPV16. Natural amino acid variation in HPV16 E6 can alter its carcinogenic potential. The aim of this study was to analyze phylogenetically E6 and E7 genes and proteins of HPV16 from Indonesia and predict the effects of single amino acid substitution on protein function. This analysis could be used to reduce time, effort, and research cost as initial screening in selection of protein or isolates to be tested in vitro or in vivo.
Methods: In this study, E6 and E7 gene sequences were obtained from 12 samples of Indonesian isolates, which were compared with HPV16R (prototype) and 6 standard isolates in the category of European (E), Asian (As), Asian-American (AA), African-1 (Af-1), African-2 (Af-2), and North American (NA) branch from Genbank. Bioedit v.7.0.0 was used to analyze the composition and substitution of single amino acids. Phylogenetic analysis of E6 and E7 genes and proteins was performed using Clustal X (1.81) and NJPLOT softwares. Effects of single amino acid substitutions on protein function of E6 and E7 were analysed by SNAP.
Results: Java variants and isolate ui66* belonged to European branch, while the others belonged to Asian and African branches. Twelve changes of amino acids were found in E6 and one in E7 proteins. SNAP analysis showed two non neutral mutations, i.e. R10I and C63G in E6 proteins. R10I mutations were found in Af-2 genotype (AF472509) and Indonesian isolates (Af2*), while C63G mutation was found only in Af2*.
Conclusion: E6 proteins of HPV16 variants were more variable than E7. SNAP analysis showed that only E6 protein of African-2 branch had functional differences compared to HPV16R.
Downloads
References
Yamada T, Manos MM, Peto J, Greer CE, Munoz N, Bosch FX, et al. Human papillomavirus type 16 sequence variation in cervical cancers: a worldwide perspective. J Virol. 1997;71(3):2463–72.
Narisawa-Saito M, Kiyono T. Basic mechanisms of high-risk human papillomavirus-induced carcinogenesis: roles of E6 and E7 proteins. Cancer Sci. 2007;98(10):1505–11. http://dx.doi.org/10.1111/j.1349-7006.2007.00546.x
Smith B, Chen Z, Reimers L, van Doorslaer K, Schiffman M, Desalle R, et al. Sequence imputation of HPV16 genomes for genetic association studies. PLoS One. 2011;6(6):e21375. http://dx.doi.org/10.1371/journal.pone.0021375
de Villiers EM, Fauquet C, Broker TR, Bernard HU, zur Hausen H. Classification of papillomaviruses. Virology. 2004;324(1):17–27. http://dx.doi.org/10.1016/j.virol.2004.03.033
Bernard HU, Burk RD, Chen Z, van Doorslaer K, zur Hausen H, de Villiers EM. Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology. 2010;401(1):70–9. http://dx.doi.org/10.1016/j.virol.2010.02.002
Muñoz N, Bosch FX, de Sanjosé S, Herrero R, Castellsagué, Shah KV, et al. Epidemiologic classification of human papillomavirus types associated with cervical cancer. N Engl J Med. 2003;348(6):518–27. http://dx.doi.org/10.1056/NEJMoa021641
hpvcentre.net [internet]. Spain: ICO Information Centre on HPV and Cervical Cancer (HPV Information Centre), [update 2014 Dec 18]. Available from: http://www.hpvcentre.net/statistics/reports/XWX.pdf
Seedorf K, Krämmer G, Dürst M, Suhai S, Röwekamp WG. Human papillomavirus type 16 DNA sequence. Virology. 1985;145(1):181–5. http://dx.doi.org/10.1016/0042-6822(85)90214-4
Hildesheim A, Wang SS. Host and viral genetics and risk of cervical cancer: a review. Virus Res. 2002;89(2):229–40. http://dx.doi.org/10.1016/S0168-1702(02)00191-0
Yamada T, Wheeler CM, Halpern AL, Stewart AC, Hildesheim A, Jenison SA. Human papillomavirus type 16 variant lineages in United States populations characterized by nucleotide sequence analysis of the E6, L2, and L1 coding segments. J Virol. 1995;69(12):7743–53.
Chen Z, Schiffman M, Herrero R, Desalle R, Anastos K, Segondy M, et al. Evolution and taxonomic classification of human papillomavirus 16 (HPV16)-related variant genomes: HPV31, HPV33, HPV35, HPV52, HPV58 and HPV67. PloS One. 2011;6(5):e20183. http://dx.doi.org/10.1371/journal.pone.0020183
Burk RD, Chen Z, Harari A, Smith BC, Kocjan BJ, Maver PJ, et al. Classification and nomenclature system for human Alphapapillomavirus variants: general features, nucleotide landmarks and assignment of HPV6 and HPV11 isolates to variant lineages. Acta Dermatovenerol Alp Pannonica Adriat. 2011;20(3):113–23.
Cornet I, Gheit T, Franceschi S, Vignat J, Burk RD, Sylla BS, et al. Human papillomavirus type 16 genetic variants: phylogeny and classification based on E6 and LCR. J Virol. 2012.86(12):6855–61. http://dx.doi.org/10.1128/JVI.00483-12
de Boer MA, Peters LA, Aziz MF, Siregar B, Cornain S, Vrede MA, et al. Human papillomavirus type 16 E6, E7, and L1 variants in cervical cancer in Indonesia, Suriname, and The Netherlands. Gynecol Oncol. 2004;94(2):488–94. http://dx.doi.org/10.1016/j.ygyno.2004.05.037
Daf S, Jena L, Kumar S. Comparative phylogenetic analysis of E6 and E7 proteins of different 42 strains of HPV. JK Science. 2010;12(1):6–10.
Pientong C, Wongwarissara P, Ekalaksananan T, Swangphon P, Kleebkaow P, Kongyingyoes B, et al. Association of human papillomavirus type 16 long control region mutation and cervical cancer. Virol J. 2013;10(30):1–9. http://dx.doi.org/10.1186/1743-422x-10-30
Bromberg Y, Rost B. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res. 2007;35(11):3823–35. http://dx.doi.org/10.1093/nar/gkm238
Katsonis P, Koire A, Wilson SJ, Hsu TK, Lua RC, Wilkins AD, et al. Single nucleotide variations: biological impact and theoretical interpretation. Protein Sci. 2014;23(12):1650–66. http://dx.doi.org/10.1002/pro.2552
Adeel MM, Qasim M, Ashfaq UA, Masoud MS, ur Rehman M, ul Qamar MT, et al. Modelling and simulation of mutant alleles of breast cancer metastasis suppressor 1 (BRMS1) gene. Bioinformation. 2014;10(7):454–9. http://dx.doi.org/10.6026/97320630010454
Lurchachaiwong W, Junyangdikul P, Payungporn S, Chansaenroj J, Sampathanukul P, Tresukosol D, et al. Entire genome characterization of human papillomavirus type 16 from infected Thai women with different cytological findings. Virus Genes. 2009;39(1):30–8. http://dx.doi.org/10.1007/s11262-009-0363-0
Bioedit software. (internet).available from http://bioedit.software.informer.com
ClustalX software. (internet).available from http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalX
NJPLOT software. (internet). available from http://en.freedownloadmanager.org/Windows-PC/NJPLOT-FREE.html
Zhang S, Wang T. Phylogenetic analysis of protein sequences based on conditional LZ complexity. MATCH Commun. Math. Comput. Chem. 2010;63:701–16.
Oppedoes F. Phylogenetic analysis using protein sequences In: Salemi M, Vandamme A-M. The Phylogenetic Handbook: A practical approach to DNA and protein phylogeny. Cambridge: Cambridge University Press. 2003. p. 210–43.
Giannoudis A, Herrington CS. Human papillomavirus variants and squamous neolasia of the cervix. J Pathol. 2001;193(3):295–302 http://dx.doi.org/10.1002/1096-9896(2000)9999:9999<::AID-PATH809>3.3.CO;2-3
Pande S, Jain N, Prusty BK, Bhambhani S, Gupta S, Sharma R, et al. Human papillomavirus type 16 variant analysis of E6, E7, and L1 genes and long control region in biopsy samples from cervical cancer patients in north India. J Clin Microbiol. 2008;46(3):1060–6. http://dx.doi.org/10.1128/JCM.02202-07
Metcalfe S, Roger M, Faucher MC, Coutlée F, Franco EL, Brassard P. The frequency of HLA alleles in a population of Inuit women of northern Quebec. Int J Circumpolar Health. 2013;5(72):1–4. http://dx.doi.org/10.3402/ijch.v72i0.21350
Berumen J, Ordo-ez RM, Lazcano E, Salmeron J, Galvan SC, Estrada RA, et al. Asian-American variants of human papillomavirus 16 and risk for cervical cancer: a case-control study. J Natl Cancer Inst. 2001;93(17):1325–30. http://dx.doi.org/10.1093/jnci/93.17.1325
Hildesheim A, Schiffman M, Bromley C, Wacholder S, Herrero R, Rodriguez A, et al. Human papillomavirus type 16 variants and risk of cervical cancer. J Natl Cancer Inst. 2001;93(4):315–8. http://dx.doi.org/10.1093/jnci/93.4.315
Xi LF, Koutsky LA, Hildesheim A, Galloway DA, Wheeler CM, Winer RL, et al. Risk for high-grade cervical intraepithelial neoplasia associated with variants of human papillomavirus types 16 and 18. Cancer Epidemiol Biomarkers Prev. 2007;16(1):4–10. http://dx.doi.org/10.1158/1055-9965.EPI-06-0670
Sichero L, Ferreira S, Trottier H, Duarte-Franco E, Ferenczy A, Franco EL, et al. High grade cervical lesions are caused preferentially by non-European variants of HPVs16 and 18. Int J Cancer. 2007;120(8):1763–8. http://dx.doi.org/10.1002/ijc.22481
Freitas LB, Chen Z, Muqui EF, Boldrini NA, Miranda AE, Spano LC, et al. Human papillomavirus 16 non-European variants are preferentially associated with high-grade cervical lesions. 2014. PLoS One. 2014;9(7):e100746. http://dx.doi.org/10.1371/journal.pone.0100746
Lichtig H, Algrisi M, Botzer LE, Abadi T, Verbitzky Y, Jackman A, et al. HPV16 E6 natural variants exhibit different activities in functional assays relevant to the carcinogenic potential of E6. Virology. 2006;350(1):216–27. http://dx.doi.org/10.1016/j.virol.2006.01.038
Downloads
Published
How to Cite
Issue
Section
License
Authors who publish with Medical Journal of Indonesia agree to the following terms:
- Authors retain copyright and grant Medical Journal of Indonesia right of first publication with the work simultaneously licensed under a Creative Commons Attribution-NonCommercial License that allows others to remix, adapt, build upon the work non-commercially with an acknowledgment of the work’s authorship and initial publication in Medical Journal of Indonesia.
- Authors are permitted to copy and redistribute the journal's published version of the work non-commercially (e.g., post it to an institutional repository or publish it in a book), with an acknowledgment of its initial publication in Medical Journal of Indonesia.
